The Merging (Sequel to The Rift)
by Sparkers16
Summary: This story is a sequel to my previous story, The Rift. Read the first one before this! When Flygon decides to stay in Equestria, everything seems perfect as everyone prepares for the Grand Galloping Gala. But soon, trouble arises. Trouble that will change the fates of Equestria and the Pokémon world forever...
1. Chapter 1: Happy Birthday

_All was quiet in the Everfree Forest. The birds chirped, the small rodents scurried around on their search for food, and large predators like timberwolves howled in the distance. _

_And suddenly, a cyan pegasus with a rainbow mane burst through the foliage, flapping her wings as fast as she could and panting hard. Rainbow Dash was running from something. Not a predator like a timberwolf or a manticore. She was flying away from something much, much worse._

_A human._

_Rainbow looked back behind her to see that the human was pulling out something from it's bag. It was a purple ball with a bottom white half. It had a small "M" engraved on it. A Master Ball. Master Balls could catch Pokémon without fail. But...Rainbow wasn't a Pokémon. Why was the human trying to catch her?_

_She looked at herself and cried out in horror. She was no longer a pony. She had green talons instead of hoofs, diamond-shaped wings instead of feathered ones, and a long, green striped tail. She was Flygon. And that meant the human could catch her. _

_Flygon desperately tried to escape the human. But she couldn't get away in time as the human threw the Master Ball at her. It opened up and a red light surrounded her..._

* * *

Rainbow Dash woke up, sweating and panting hard. The nightmares were progressively getting worse. They always had to do with her getting captured by humans.

She looked out of her bedroom window. The sun was just rising. It was extremely early in the morning.

_Come on, Ari, _Rainbow thought. _You could've woken me up later. You know I like to sleep in when I don't have weather duty. _

After a few seconds, a reply came from Rainbow's mind. _I wake you up from your nightmares almost every night. I think I deserve a thank you._

_Whatever, _Rainbow muttered in her head. Ari, the spirit that resided inside her mind, could be a real pain sometimes. It had been two months since he'd started talking to her. Two months since she traveled to the Pokémon world.

_Besides, _Ari continued, _someone is at your door._

Sure enough, Rainbow heard a knock on her door. "Just a minute!" she yelled. Rainbow got out of bed, ran a brush through her mane, put some food in her pet tortoise, Tank's bowl, and zoomed to her door.

She opened the door and gasped. There were her five best friends, floating in front of her house in a balloon!

"HAPPY BIRTHDAY!" They all shouted.

"What the...is this a prank?" Rainbow said, dumbfounded.

"No, silly!" Pinkie Pie squealed. "It's your birthday, and we're gonna party all day long!"

"Oh, yeah, it IS my birthday!" Rainbow said, face-hoofing. "I was wondering why I had weather duty off on a Thursday."

"No matter," Rarity smiled. "We have the whole day planned out for the birthday mare! First, we're going to the park to have breakfast."

"That sounds great," Rainbow glided down to the ground from her cloud house. "You guys are the best!"

Throughout the day, Rainbow and her friends traveled around Ponyville. They played party games, cheered as Rainbow showed of her new flying stunts, and hung out by the park. At evening, they all went to a restaurant and had dinner.

After the six of them finished eating, Pinkie stood up. "I have to get the cake from Sugarcube Corner! While I'm gone, you guys tell Dashie about the very special visitor who's coming!"

"What visitor?" Rainbow questioned her friends as Pinkie bolted away.

"Somepony is coming to Ponyville to celebrate your birthday," Fluttershy answered vaguely.

"Somepony ya haven't seen in a mighty long time," Applejack added.

"C'mon, I need more hints than that."

"Well, it is someone who has traveled far to get here," Rarity admitted.

"Somepony who traveled far to get here..." Rainbow thought out loud. "Oh, is it Little Strongheart? She came all the way here from Appleloosa?"

"No, not her," Twilight shook her head. "Farther than that."

"Um...is it Zecora? Or Shining Armor, or Princess Cadence, or Spitfire, or Discord?" Rainbow shuddered at the thought of the draconequus, who had recently become more friendly with them all, especially Fluttershy.

"Nope, none of them," Applejack sighed.

"Ok, I need another hint. Just how far has this person come?"

"Very, very far," Fluttershy said.

Just then, Pinkie came back, carrying a box from Sugarcube Corner. "More like, very very very very very very very very very very very very far!"

"As in, between dimensions," Twilight said, giving away the answer.

"Wait...you can't be talking about..."

Just then, a tiny white dot appeared several feet off to the side. Rainbow recognized what it was immediately. A portal. Rainbow's heart pounded as she remembered that portals cause gigantic explosions when activated. "Get under cover!" she screamed, diving down beneath the table.


	2. Chapter 2: Flygon's Return

Rainbow trembled under the table, bracing herself for the explosion.

"Uh...what're ya doing?" Applejack, whispered, bending down.

"Ooh! Are you playing Hide and Seek?" Pinkie guessed.

"Th-the portal!" Rainbow stuttered. "It's gonna explode!" She pointed to the white dot, which was growing in size quickly.

But once the portal reached maximum size, there was no explosion. Instead, a pony just jumped out from it, and the portal disappeared. This pony was a pegasus. She had a pea-green coat and a dark green mane tipped with pink.

"Hey, guys!" she waved her hoof.

It took a second for Rainbow to recognize the mare. "Flygon!" she exclaimed, jumping from the table and giving the mare a hug. "I can't believe you finally came! It's been two whole months, and I've been worrying about you like crazy! What took you so long?!"

Flygon laughed. "Slow down, Rainbow. I just got here. Inter-dimensional travel is tiring!"

Rainbow stepped back, embarrassed. "I just have so many questions!"

"Ask away," Flygon replied, stretching out her feathered wings.

"Okay. Why didn't the portal explode?"

"I've made some...modifications to the portal machine," Flygon said. "Now, it won't explode upon activating."

"Wow, I keep forgetting that you're some sort of genius," Rainbow commented. "Alright, next question. Why haven't you visited in two months?"

Flygon frowned. "For some reason, the portal machine wasn't working very well. I kept trying to make a portal, but nothing happened. Then, Latios, Latias, and I figured out that the machine only works in certain places. Sort of like a wi-fi signal."

"A what signal?" All the ponies chorused.

"Never mind," Flygon chuckled, remembering that Equestrian technology wasn't quite as advanced as her world. "Any other questions?"

"How long are you staying?"

"Well," Flygon began, "I was thinking that I wasn't really safe in the Pokémon world, with humans trying to capture me and everything. So I thought that I should stay in Equestria long-term. Maybe even...permanently."

"YOU'RE STAYING?" Rainbow shouted in disbelief. "Omigosh, this is the best thing ever! Finally, one of my best friends isn't stuck in another universe!"

"And the Grand Galloping Gala is coming soon as well!" Rarity jumped up in excitement. "Oh, my, I'll have to design a new dress for you!"

"The...Grand Galloping Gala?" Flygon repeated.

"It's this huge, fancy-pants party up in Canterlot," Applejack said.

"Interesting," Flygon shrugged. "Any other questions?"

"Where are Latias and Latios?" Rainbow asked, looking around, expecting another portal to appear.

Flygon looked around in confusion as well. "I guess they didn't jump into the portal in time. Hopefully, they'll be here soon. Anyway, Twilight told me there'd be cake here. I've never had cake before. Can we have the cake now?"

Pinkie gasped. "You've never had CAKE before? Oh, no!"

"Hold on a sec," Rainbow interrupted. "Have you and Twilight been talking?"

Twilight stepped forward. "Actually, yes. I've been using the spell Princess Luna taught me to walk in dreams. Flygon and I have been communicating this way."

Flygon nodded. "Once we found a place where the portal machine worked, Twilight had me come on your birthday as a surprise."

"Awesome!" Rainbow smiled warmly. "You guys really are the best friends anypony could have!"

"Of course we are," Rarity said with a toss of her mane. "Now, let's sing Happy Birthday!"

Pinkie took the cake out of the box. "I baked it myself!" she squealed. The cake looked exactly like Rainbow's cutie mark. Pinkie materialized several candles and placed them on the cake. After lighting them, the ponies sang.

"Happy Birthday to you, Happy Birthday to you, Happy Birthday to Rainbow Dash, Happy Birthday to you!"

"Are ya one, are ya two, are ya three," Applejack continued.

"Shh!" Pinkie silenced her. "We're not supposed to give out our ages to the readers!"

**_"Pinkie, stop breaking the fourth wall!" the author yelled._**

Pinkie stuck her tongue out at the author while everybody else stared at her.

"Just ignore it," Fluttershy whispered to Flygon. "Pinkie does that a lot. She thinks we're in some sort of story."

"Alright, blow out the candles and make a wish!" Twilight suggested to Rainbow.

Rainbow thought about her wish before blowing out the candles. _I wish that I'll join the Wonderbolts!_

Suddenly, she heard Ari's voice. _You should know that wishing for your dreams doesn't make them happen. You have to make them happen yourself._

_Ugh, fine, _Rainbow rolled her eyes. _If I can't wish for my dreams, I wish...you know what? I don't need a wish. This has been the best birthday ever!_

Satisfied, Rainbow took a deep breath and blew out the candles.

* * *

**_Author's Note: Yay, I finally finished a new chapter! Sorry if you guys didn't like the fourth wall break. I just thought it would be really funny. :P_**


	3. Chapter 3: Fashion Sense

One week later...

* * *

"Stand still, Flygon!" Rarity growled as she used her magic to measure the pegasus with a measuring tape.

"I need to fly," Flygon muttered. She just didn't feel safe standing around like this.

"You're just like Rainbow Dash," Rarity scowled. "Could you please just stand still a minute longer? Then, you can go while I design the dress."

"Fine," Flygon sighed, letting Rarity poke and prod her. Flygon was standing in Carousel Boutique as Rarity made her a dress for the Gala.

"Done," Rarity wrote down a few notes on a pad of paper, and put the measuring tape away. "Now, what kind of dress are you hoping for?"

"Uh, I don't know. I've never worn a dress before."

Rarity gasped. "Never worn a dress? How?!"

Flygon rolled her eyes. "In my world, Pokémon don't wear clothes." She was starting to realize that ponies were more like humans than she'd thought. She shook the thoughts from her head. She knew that her Equestrian friends weren't as evil as humans. But they were still similar. And it bothered her.

"Very well, then," Rarity dismissed. "Let me draw a quick sketch." The unicorn took a pencil and drew on a piece of paper for a moment. Then, she showed Flygon the paper. The dress was close fitting, with a diamond pattern on the train.

"Um...I'm not sure I like it," Flygon admitted. "Can I try making a sketch?"

Rarity bit her lip. "Fine," she muttered, handing Flygon the paper and pencil with her magic.

Flygon awkwardly held the pencil in her mouth. She was used to manipulating objects with her claws. She erased Rarity's drawing, and made one of her own. She made a simple, plain dress, with a very short train.

"Sorry if it's a bit messy," Flygon shrugged as she explained the dress, still drawing. "See, I want it to be aerodynamic and light just in case I need to make a quick take-off. And it should have a lot of pockets. And shoes with good grips. Oh, and maybe it can be camouflage!"

Rarity stared at Flygon's drawing. "You do know that this is a formal event, not a war, right?"

"Yeah, but it's my dress," Flygon rolled her eyes. "Shouldn't I get whatever I want on it?"

Rarity suppressed a scream of rage. "You...you...AGGH!" She stormed out of the room.

Flygon stood there for a while, confused. Did she say something wrong? It only made sense for her dress to be the way she wanted...right?

"Hey, Flygon," said Rainbow Dash, walking into the room. "How's the dress coming along?"

"Not so good," Flygon frowned. She told Rainbow what had happened.

"Uh oh," Rainbow gulped, hearing the faint sound of Rarity sobbing from the upstairs room of the boutique. "How about we go get some lunch? I think Rarity needs some alone time."

"Sure," Flygon agreed, leaving with Rainbow.

The two of them flew to a restaurant in Ponyville, where they ordered salads.

"What's up with Rarity?" Flygon asked, chewing on her lettuce.

"It was this whole thing that happened last year," Rainbow explained. "Rarity made us dresses for the Gala last year, too. But we got carried away and made them all ugly. And then, we ended up almost ruining her fashion career. The original dresses she designed were totally better. It's best to trust her judgment."

"Oh..." Flygon hung her head in shame. "I guess I did get carried away. My bad."

"You should really go apologize," Rainbow narrowed her eyes at Flygon.

"I should," the green pegasus agreed. "I'll go back right now," she said, finishing her salad.

"Great," Rainbow took another bite of her food. "I'll be there in a flash. Don't worry, the bill's on me."

"Bill?" Flygon turned around.

"Uh, yeah," Rainbow said. "When you buy something, you have to pay for it."

"Then I'll need my own money," Flygon declared. "I can't let you guys pay for everything."

"I'll see if I can get you a job on the weather team," Rainbow suggested. "Now, go!"

"See you later!" Flygon shouted, flying back to the boutique as fast as she could.

She gingerly stepped into the store. Rarity was back downstairs, looking back at the drawing Flygon made.

"Oh, hello, Flygon," Rarity turned around. Her eyes were red and her muzzle was wet. She was crying. "I'm truly sorry for my little outburst. I promise I will make the dress you wanted."

"No, Rarity," Flygon grabbed the drawing and ripped it into pieces. "You should make the dress you originally wanted. I was wrong. I should listen to you. You're the professional here, after all."

Rarity smiled widely. "I'm glad you've come to your senses. Now, let's get back to work!"

* * *

_**Sorry if this chapter is mostly fluff! Read n' Review!**_


	4. Chapter 4: At the Gala

"Now, open your eyes!"

Flygon opened her eyes and looked in the mirror at her new dress. It was beautiful. The dress was dark green and close-fitting near her chest, with holes for her wings. The train was long, and covered with glimmering, diamond-shaped pink and green scales. Her hooves were comfortable in soft, magenta boots. Atop Flygon's head sat a small, silver crown with emeralds.

"Oh, Rarity, it's amazing," Flygon cooed. The dress fit her perfectly, and wasn't too big and frilly. Flygon could take to the air in it if she needed to.

"I'm glad you think so," the white unicorn called from the other room, where everypony was changing into their dresses. It was the day of the Gala.

And then, the others came in, too. Rarity had designed them dresses as well.

Rainbow Dash's dress was crimson red, with deep blue and golden sashes running across it. She wore a necklace with rainbow pearls. Her mane was braided with gold ribbons.

Twilight's dress was layered with fabrics of purple, pink, and white. She wore her princess crown on her head, and her mane was styled into a bun.

Pinkie's dress was sky blue and frilly. It was studded with stars of pink and yellow. A star pin combining all those colors was in her fluffy, pink mane. Confetti bits were stuck in her mane as well.

Applejack wore an orange and red, fringed dress. On the red parts, there were orange apple designs, and vice-versa. The edges were tipped with green. Much to the farm pony's dislike, her mane was curled under a fancy hat.

Fluttershy's dress was a turquoise color. It was glittery and see-through. Layered over the see-through part, there was deep pink fabric, meant to represent flower petals. She wore a flower crown, with pink and yellow daisies.

And finally, Rarity stepped into the room. She wore a stunning white gown, layered with gold, silver, blue, and purple. Each layer had different gemstones on it: topaz, sapphires, amethyst, and diamond. Atop her head sat a glass crown, studded with a single blue diamond. The unicorn had to fend Spike off; he kept trying to eat her dress.

Everypony marveled at their gowns, thanking Rarity many times. Then, a honking sound could be heard outside.

"There's the carriage we're taking to Canterlot!" Rarity exclaimed.

"We'd better be catchin' it now if we don't wanna be late," Applejack mused as everyone ran outside and hopped into the carriage.

As the carriage pulled by several stallion from Ponyville bumped along the mountainous road to Canterlot, everyone discussed what was going to happen at the Gala.

"Well, we learned last year that it's better to be with friends than go chasing your own far-out dreams," Fluttershy offered.

"Yeah," Spike agreed, pinching his nose so that he wouldn't be tempted by all the gems on the dresses. Flygon realized that she felt a little tempted to eat the gems as well. Maybe because she was a Dragon type, she had the urges of a dragon in Equestria.

"This year, we're gonna stick together!" Rainbow agreed, flying upwards and hitting her head on the roof of the carriage. She laughed nervously and sat back down.

Soon enough, the eight of them arrived at Canterlot, a gleaming marble castle perched on the side of a mountain. It was nighttime, and fireworks of all different colors illuminated the black sky. They all walked into the castle.

There, they were greeted by a large alicorn with a white coat and a multicolored, flowing mane.

"Flygon, this is Princess Celestia," Twilight introduced. "She rules over all of Equestria."

"Ah, yes, Flygon, is it?" The princess smiled warmly. "I've heard much about you from Princess Twilight Sparkle. How is Equestria faring for you?"

"Very well...Your Highness," Flygon answered truthfully, bowing.

"That's wonderful," Celestia said. "It's amazing to be able to show off our country to a newcomer. Have fun at the Gala!"

"Thank you," Flygon dipped her head, walking off to the party room along with her friends. Flygon wasn't so sure she trusted Princess Celestia. Her kindness just seemed...fake. Exaggerated. Flygon had a feeling the princess wasn't so nice under that gleaming white fur and sun cutie mark.

The eight friends talked, danced, and got their pictures taken with famous ponies Flygon didn't know. As the moments raced by, Flygon felt that she was beginning to feel hot and uncomfortable. Her heart was pounding quicker than usual. As the friends sat down to eat dinner, the heat was becoming hard to handle.

"I...I need some fresh air," Flygon said to everypony else.

"C'mon, sugar cube, we just sat down," Applejack sighed.

"You can't party on an empty stomach!" Pinkie added.

Fluttershy stood up. "I'm not that hungry, either. How about I go show Flygon the castle garden?"

"Alright," Rainbow said, stuffing a pastry in her mouth. "Meet us back here soon!"

Flygon and Fluttershy walked outside into the Canterlot garden.

"Um...are you okay, Flygon?" The pegasus asked quietly. "You look kind of nervous."

The cool, night air seemed to help the heat, but soon the burning came back. "I'm fine," Flygon lied. "The castle was just a bit crowded."

"I agree," Fluttershy breathed. "I hate crowds."

The two of them walked deep into the garden. They found themselves deep in the dark green foliage, next to a babbling brook. Nopony else was there.

"Look, there are the animals!" Fluttershy pointed. Swinging in the trees, swimming in the brook, there were all sorts of animals. They reminded Flygon of Pokémon. That one looked a bit like a Mankey, that one HAD to be a Pidove, that one resembled a Froakie. Fluttershy flew up to take a closer look, and all the animals scattered.

"Darn it," she whimpered. "They did that last year, too."

"I thought you had a talent with animals," Flygon said.

"I do. But these ones always run away."

Flygon looked up in the trees. She spotted a few animals, cowering. She wondered if they were happy in the garden, or if they were being kept there against their will.

Flygon shared her thoughts. "Maybe the animals are scared because they're trapped here."

"Probably," Fluttershy glided back down. "I never thought of that before. I bet Princess Celestia put up a magical shield to make sure they didn't escape."

"Yeah," Flygon trailed off. All she could think off was how these animals were just like Pokémon, being trapped in this garden to gawk at. "We should free them," she blurted out.

"Oh, I wish we could," Fluttershy sighed. "But we would get in huge trouble."

"I guess. It's just...this reminds me so much of my world." Flygon explained her thoughts to Fluttershy.

For a while, the soft yellow pegasus took the information in. "Flygon?" she asked, her voice near impossible to hear. "Do you want to go back to your world?"

"No," Flygon said matter-of-factly. "I don't. It's too dangerous there for me. But...you ponies keep making me think of humans. And the more I think of humans, the more I think it's so unfair for them to imprison innocent Pokémon!" By the end, Flygon was shouting. The burning was even stronger than before. It was unbearable. Flygon gave in, letting the flames in her blood consume her.

Something was wrong.

Something was very, very wrong.

The burning feeling was gone. Fluttershy was staring at her with a mixture of surprise, disgust, and pure terror. "D-D-DRAGON!" she screamed, hiding behind a tree.

"What?" Flygon looked down at herself and gasped. Red casings covered her eyes. Her wings were diamond shaped. She had scales instead of fur. Her tail was long, and fanned out into three diamond shapes. She was back in her Pokémon form!

"P-P-Please d-don't eat me!" Fluttershy cried.

"Fluttershy, it's me!" Flygon shouted. "I don't know why, but I'm back in my Pokémon form!"

Fluttershy's head poked out from the tree. "Flygon? You're a d-dragon?"

"Normally, yes," Flygon nodded. "But I don't want to hurt you, trust me!"

"But why did you turn back?" Fluttershy flew forward.

"I have no idea," Flygon bit her lip, trying to get used to her normal form again. After a few seconds, the burning feeling returned. The fire burned much shorter this time. And when it stopped, Flygon was a pegasus again.

"Thank Celestia," Fluttershy wiped her forehead with one hoof. "That...startled me."

"Oh, no! Rarity's dress!" Flygon gasped. The dress had ripped when Flygon turned into a Pokémon.

Seeing the ripped dress, Fluttershy seemed to steel herself. "I can fix that up quick," she said. "Stay right there!" Before Flygon could say anything, Fluttershy zoomed off. She returned with a needle and thread after a minute. Immediately, the pegasus went to work, stitching up the tears in the dress. By the time she was done, the dress looked as good as new.

"Wow, Fluttershy!" Flygon praised, sliding the dress back on. "Rarity would've killed me if she found out I ruined it."

"Oh, it was nothing," Fluttershy said sheepishly. "I've always loved sewing."

Flygon's stomach rumbled. "Let's go find everypony else. I'm getting hungry!"

Fluttershy frowned. "But...what if you turn into a dragon again in front of everypony?"

"We'll just have to hope that doesn't happen," Flygon said, walking back to the castle. Fluttershy followed her. "And we'd better not tell anyone about this."

The rest of the night was pretty uneventful. Thankfully, Flygon didn't turn back into a Pokémon again during the Gala. Rainbow, Twilight, Rarity, Fluttershy, Spike, and Pinkie all agreed that they had the best night ever at the Grand Galloping Gala. As for Flygon, she wasn't so sure.

* * *

_**Okay, I revised the chapter, and now I think it's MUCH better. For the people who read the original Chapter 4, please just forget about it. **_


	5. Chapter 5: Fabric and Needles

Flygon yawned as she woke up early in the guest bed at Twilight's library, where she was staying. Rainbow got her a job on the weather team, and she had to report to Cloudsdale to help create a rainstorm.

The Gala went on until midnight last night, and Flygon was incredibly tired. She forced herself to get up, rubbing her eyes with her claws.

Claws?

Uh oh. She was in her Pokémon form again! Why had this happened again? Last time, the Pokémon transformation only lasted for a few seconds. So maybe it would wear off soon. And just as Flygon predicted, after a while, she felt a burst of heat and she was a pegasus again. But she did notice that she was a Pokémon for longer than last time. Fluttershy already knew, but Flygon had to tell everypony else. She might as well start with Twilight and Spike, who were sleeping across the room. Flygon walked over to Twilight's bed, tripping a couple times, because she was used to being a Pokémon again.

"Twilight, wake up," Flygon whispered, poking her with one hoof.

"Flygon?" Twilight murmured sleepily. "Are you going to your weather job?"

"I don't think I can. Twilight, I think there's something wrong with me."

Instantly, Twilight leaped out of bed. "What's wrong?"

"I keep turning back into my original form. You know...a Pokémon."

"Hm." Twilight took a minute to ponder that. "I really have no idea why that could be happening. But I think it's a serious problem, and we should tell Princess Celestia about it."

Princess Celestia? Oh, great. Flygon was still unsure about trusting that white alicorn. "Alright," Flygon agreed, keeping her feelings to herself. She knew how much the ponies looked up to the princess.

"Spike, wake up!" Twilight said, shaking the baby dragon.

"Mmh?" said Spike, rolling over on his tiny bed.

"We need to write a letter to Princess Celestia!"

"I'm up, I'm up," the dragon stood up, giving a huge yawn.

"Okay, let me write this letter. Flygon, describe what's happening to you."

"Well," Flygon started, "I keep feeling really hot, like my blood is burning. Then, when I open my eyes again, I'm in my Pokémon form."

"Fever...transformation..." Twilight breathed as she wrote, using her magic to levitate a quill. "Good. I've gotten it all down. Here you go, Spike." Twilight rolled up the paper and tied it with a red ribbon. She handed it to Spike, who breathed green fire on it, burning the paper to ashes that floated through the window.

"Why did you burn the letter?" Flygon cried.

"I didn't really burn it," Spike explained. "Twilight enchanted me so if I breathe fire on a letter, it gets sent to Princess Celestia."

Jus then, more ashes floated into the room. They collected together, and materialized into a letter. Twilight grabbed the letter and read it.

"The princess wants us to come to Canterlot," Twilight gasped. "Spike, you stay here and watch the library. Flygon and I have to go right now."

"Sure thing," Spike said, flopping back down on his bed and falling back asleep.

Flygon and Twilight rushed out of the library. "Can Rainbow come, too?" Flygon asked as they passed the cyan pegasus's cloud house.

"I guess. Go wake her up," Twilight ordered.

Flygon opened her wings and flew into Rainbow's house. There, she found Rainbow sleeping soundly on her bed. Flygon knew there was no subtlety when dragging Rainbow out of bed. "Wake up!" Flygon shouted in her ear.

"Huh? Flygon?" Rainbow opened her eyes. "What's up?"

"We're going to Canterlot," Flygon announced. "We have to see Princess Celestia."

"Why? Is there something wrong?"

"I'll tell you on the way," Flygon replied.

The three ponies ran to the train station, and caught the early train to Canterlot. While they were on the train, Flygon explained everything that was happening to Rainbow. Just as she finished, Flygon felt another rush of heat.

"I'm about to transform again," Flygon warned.

"Don't worry, we're alone," Rainbow said, looking around. The train car they were in was empty.

As the burning overtook Flygon, Twilight ran forward and shoved a thermometer in her mouth. "A fever of 112," the purple alicorn said, shocked.

Flygon closed her eyes as the flames consumed her. When she opened them, she was a Pokémon again.

"Whoa," Rainbow's eyes widened. "I never thought I'd see you like this again."

"Me neither," Flygon sighed, flicking her striped, reptilian tail. "And the transformations are getting longer. I think I'm eventually going to transform...permanently."

The two ponies and the Pokémon all sat in silence as they took that in. If Flygon became a Pokémon permanently, she wouldn't be able to function in Equestria. They would think she was a monster. After a few minutes, Flygon reverted to a pegasus again. Over the course of the hour train ride, Flygon transformed three more times, each transformation spanning more time than the one before it. By the time the train arrived at Canterlot, Flygon was thankfully a pony.

"We need to get to the castle, quick," Flygon whispered as the three traveled through the crowds of Canterlot. They were moving so slow, another transformation would come while they were still trying to shove through the masses.

"C'mon, let's fly," Rainbow said, hovering in the air.

Twilight stopped the pegasus using her own wing. "This is Canterlot! Nopony can just fly through the streets. It's disrespectful."

"But this is an emergency!" Rainbow protested.

Twilight gritted her teeth, deep in thought. "Well, I guess we have to," she sighed.

The three of them took to the air and zoomed over the populace towards the castle. Flygon heard the murmurings of the residents of Canterlot as they recognized Princess Twilight Sparkle doing something that was highly frowned upon. "What an uncouth, immature filly." "She shouldn't be leading Equestria if she can't even be patient." Flygon saw a couple tears stream out of Twilight's eyes, and instantly felt guilty for the budding princess. But then, another rush of heat came, and Flygon forgot this as they frantically raced to the castle.

As they arrived at the palace gates, the guards gasped as they saw Twilight. "Princess Twilight!" they cried. "Have you come all the way from Ponyville?"

"Yes," Twilight answered, landing in front of the guards. "We need an audience with Princess Celestia and Princess Luna. It's urgent." Princess Luna? All these new names were leaving Flygon's head spinning.

"Of course, Your Highness," the guards allowed them in, bowing. "But we're afraid Princess Luna is not in the palace currently. She's off doing royal business."

"That's fine," Twilight said, galloping through the door. Rainbow and Flygon followed. Flygon was trying her hardest to suppress the burning, but she couldn't hold on much longer.

They ran into the throne room, where Celestia herself sat on her throne. Rainbow bowed to the princess, and Flygon reluctantly bowed as well.

"Princess Twilight," Celestia addressed. "I read your letter. Flygon, have you reverted to your Pokémon form since the letter was sent?"

"Yes," Flygon stated. "Four times since then. And, well, I think I'm about to do it again."

Celestia's eyes widened. "Go ahead, then. I'm curious."

"Alright." Flygon closed her eyes and let the heat overtake her. As usual, she was a Pokémon when her eyes opened.

"I...see," Princess Celestia breathed. She looked shocked, but it seemed as if she knew something.

"What's wrong?" Rainbow asked.

"I have a theory why Flygon is transforming back into her original state," the white alicorn explained. "But I need more evidence. We need to travel to where the rift is."

"It's not a destructive rift," Flygon assured. "Just a harmless black dot."

Celestia nodded. "That's good. But I still have to see the rift."

"But there aren't any trains going back to Ponyville for a while," Twilight said.

"Then we'll teleport," Celestia smiled, her horn glowing bright yellow.

Before they knew it, they were all surrounded by a bright, yellow light. Flygon felt the oddest feeling, as if she was being sucked through a tunnel at incredible speeds. And when the light disappeared, they were in the orchards of Sweet Apple Acres, and Flygon was a pegasus again.

"Which way is the rift?" Celestia asked.

"This way," Twilight said, leading everyone to the back of the orchard. The rift Flygon made when traveling to Equestria was harmless, but just in case it started to destroy matter, Applejack surrounded it with a concrete wall. And there, inside the concrete, was the rift, which was supposed to look like a floating, black dot the size of a pebble.

But it was gigantic. The size of an apple tree.

"Oh, no," Rainbow gritted her teeth. "Is the rift...going to destroy the world again?"

"No," Flygon shook her head. "Look, the air around it isn't distorted. And it's not sucking stuff in."

"Flygon is right," Princess Celestia agreed. "There's another reason why it's enlarging like this."

Just then, another bout of fever spread through Flygon. She sighed as she turned into a Pokémon yet again. This was getting tiring. When she opened her red-cased eyes, she saw everypony was staring at the rift in shock. Flygon looked and gasped. The rift wasn't black anymore. It was white. It had turned into a portal.

"What does this mean?" Rainbow asked, dumbfounded. "Why did the rift turn into a portal when Flygon transformed?"

"This proves my theory right," Celestia sighed.

"What's your theory?" Flygon turned to the giant alicorn.

Princess Celestia stared at the portal that used to be the rift and explained. "Flygon, Rainbow Dash, you've traveled between the two universes numerous times. Now, I want you to imagine that the two universes are pieces of fabric, and you're sewing needles with thread."

"This would be much easier to explain to Rarity," Rainbow muttered.

Celestia continued. "Every time you, the sewing needles, dimension-travel, you make a stitch between the two universes, the pieces of fabric. And when you stitch together two pieces of fabric..." Celestia trailed off.

"The fabric comes together," Flygon, Rainbow, and Twilight finished, their jaws dropping.

"Exactly," Celestia nodded. "The two worlds. They're connecting."


	6. Chapter 6: The Merging

"Ooh, I'm so nervouscited!" Pinkie Pie squealed, bouncing continuously. All the ponies of Ponyville were standing in front of the flashing rift-portal, which was growing bigger. Princess Celestia said that it would grow larger and larger, until the two worlds merged.

"Me too," Twilight chuckled. "I can't wait to see what the Pokémon world is like. I only wish Princess Celestia didn't have to go back to Canterlot so she could see the connection with us."

"Well, I reckon she had to go tell all them Canterlot ponies about the merging," Applejack reasoned. "How's it coming, Flygon? Y'all seem awfully quiet."

"I'm fine. Just a little bit uncomfortable." Flygon was transforming at rapid speeds now.

"Of course you don't feel so well!" Fluttershy sighed. "I feel so bad for not noticing."

"Don't worry about it, Fluttershy. I just need a little alone time, okay?" Flygon muttered, walking off.

Rainbow flew in front of her. "Are you sure you're okay? You should be excited! Now, you can be with us and your friends from your world without all that annoying dimension traveling!"

"Oh yeah, I bet you're excited, Rainbow Dash. I'm sure you can't wait to start making out with your boyfriend!"

Rainbow stared at her, aghast. "Latios is NOT my coltfriend!" Flygon was referring to the time when Rainbow had kissed Latios, guardian of the Elements of Pokémon. "What the hay is wrong with you, Flygon?! Why are being so mean?"

"Maybe because you aren't caring about my welfare!" Flygon shouted, attracting the attention of all the nearby ponies.

"I have no idea what you're talking about!" Rainbow retaliated.

"You...don't know what's going to happen?"

"Um...no," Rainbow gave Flygon a look.

"We need to talk in private for a bit," Flygon whispered. The two of them flew away from all the ponies, who were staring at them arguing.

"Rainbow, you do know that the worlds are connecting now, right? That we'll be able to just walk from Equestria to my world with ease?" Flygon asked once they were far enough away.

"Well, duh," Rainbow snorted.

"You're not getting it," Flygon said, exasperated. "Creatures from this world will be able to come into my world. Creatures from my world will be able to come into this world. And these creatures aren't just limited to Pokémon."

"You can't be saying..." Rainbow frowned as the explanation began to dawn on her.

"Humans are coming to Equestria." Flygon finished her sentence.

"No!" Rainbow gasped, thinking of all those nightmares of the humans capturing her, torturing her, enslaving her...

"Yes." Flygon confirmed.

"What do we do?! I don't wanna get captured!"

"They can't capture you, Rainbow," Flygon said. "You're a pony, not a Pokémon. But I'll be in danger. Remember what happened when you were in my universe?"

Rainbow nodded. Flygon had been captured by a Pokémon Trainer named Ash. Rainbow, Latios, and Latias were able to rescue Flygon, but she was still bound to the Pokeball she was captured in. If Ash ever found her, she would go back to being a mindless slave. "I'm so sorry, Flygon," Rainbow said, putting her hoof around the Pokémon.

"Don't be sorry," Flygon pushed Rainbow's hoof away.

"Isn't there something we can do? Maybe the Elements of Harmony can stop the worlds from connecting!"

Flygon shook her head. "I've been reading on the Elements since I've been staying at the library. They're powerful, but they can't move entire universes. We'll just have to see what happens."

"Alright," Rainbow said slowly. "Let's go back to the others. I guess we'll want to be ready when the merging happens." The two of them flew back to the flashing portal, which was now the size of a full-grown dragon. They stood with the other ponies of Ponyville as the portal grew bigger and bigger, blinking faster and faster. The portal turned into a glowing wall that stretched as far as the eyes could see. Rainbow gritted her teeth as the wall began to fade. And when it had disappeared entirely, there was...another world beyond where the wall was. This world was covered in jungle, and Rainbow could already see a few small Pokémon in the distance.

The other ponies made way into the new world for Flygon, who was now in her Pokémon form. The message was clear: this is your home. Go back to it. Flygon gulped and walked forward. Rainbow saw her friend nervous, and she ran up to walk side-by-side with her. The two of them took the first step into the Pokémon world together. And just like that, chaos ensued. The population of Ponyville (which is larger than one might think) began to run around. Many of them stampeded back to Ponyville from Sweet Apple Acres, but a few brave ponies crossed the border to explore. They were instantly met by Pokémon. Thankfully, the Pokémon weren't hostile, curiously sniffing the new arrivals. Some of them even began to warm up to the ponies. Rainbow and Flygon had to stifle a giggle as they watched a Growlithe give Applejack a lick, much to Winona's jealously.

"These Pokémon are amazing!" Twilight grinned. "I can't wait to study them!"

"Study this!" cawed a Murkrow from above, swooping down on the purple alicorn. Of course, this only made Twilight more interested. "Wait up!" she yelled as she ran after the sinister-looking bird.

"I must say, they are quite visually impressive," Rarity admitted, staring in awe as a Milotic submerged from a nearby pond. "Idea! I'll design a new line based on them!"

"Oh...oh my!" Fluttershy squeaked as many small Pokémon surrounded her, crying, "Yay! New friend!" It seemed like she had the same connection with Pokémon as animals. "How many kinds of Pokémon did you say there are, Flygon?"

"Hundreds, as far as I know," Flygon answered.

"Hundreds?" Pinkie echoed. "Woohoo! That means hundreds times the fun!" She bounced off to join the others.

"They seem to be taking this well," Flygon joked.

"You know what?" Rainbow nudged Flygon's scaly side. "It's going to be dangerous, with all the humans pouring in, but something tells me that this whole 'worlds connecting' thing is going to turn out good in the end."

"Yeah," Flygon agreed. "I'm getting that feeling, too."

How wrong they were.


	7. Chapter 7: Humans

Flygon had a fitful sleep that night. Although she was comforted by the familiar sounds of Woobat and Noibat swooping outside the window of the library, she was still worried sick about what was going to happen. She knew that the humans would come soon...but when?

That morning, Flygon and Twilight awoke to Spike burping a letter out of green fire.

"What does it say, Spike?" Twilight yawned, straightening out her messy mane. She must have gotten a rough night's sleep as well.

"Ahem," the purple dragon began to read the letter.

_Dear Princess Twilight Sparkle,_

_As you must have seen, the merging between the two universes has gone relatively well. Nopony has been hurt, and my guards are in the process of spreading the news to all of Equestria. __But that is not why I write to you today. Last night, after the connection, several strange creatures arrived at the castle. They stood on two legs and called themselves "humans." These creatures thankfully spoke our language, and we were able to communicate with them. The humans came in peace, and although they were confused and irritated as to what had happened, they did not mean us any harm. They showed us how they were able to capture Pokémon in little capsules called "Pokeballs." Luna and I were at first skeptical about the effects of being captured on Pokémon, but the humans proved that their Pokémon enjoyed being tamed. The humans have struck a deal with us, that we provide them sanctuary and hospitality in Equestria in exchange for the usage of Pokeballs. I wish to agree to this deal, but of course, I want your thoughts on the matter, as you are an equal to Luna, Cadence and I. _

_Sincerely, Princess Celestia_

The pony and the Pokémon stood there, silent. "I guess I...forgot to tell Princess Celestia about the dangers of humans," Twilight said weakly after a while.

"NO! TELL HER NO!" Flygon shrieked.

"I will, but," Twilight started.

"But what?!" Flygon interrupted. "You know that humans are evil! Saying yes to this deal will ruin everything!"

"Then why did the captured Pokémon react positively to the humans?" Twilight countered.

"Because they were hypnotized!" Flygon snarled. "I know what being captured is like, Twilight! It's not all sunshine and rainbows! Imagine being put in a trance, having to brutally fight against your will!"

"Okay, okay, I get it!" Twilight sniffed. "But even if I disagree, I can't just forbid the other princesses from taking this deal. It's clear that the three other princesses want to accept."

"You have to try! If they accept the deal, I'll be in even more danger!"

"I know," Twilight agreed. "Spike, take a letter. Tell Princess Celestia that I strongly disapprove of this deal. According to native Pokémon, humans cannot be trusted."

"Got it," Spike said, wrapping the letter and sending it with his fire. A few seconds later, he burped up another letter. "The Princess wants you two to go to Canterlot and discuss the matter. Deja vu, much?"

"At least she's considering to refuse," Twilight frowned. "Okay, let's go catch the train."

"Actually, Twilight, I think we should just fly," Flygon suggested. "I'm not a pony anymore, remember? They probably won't even let me on the train."

"You're right," Twilight admitted. "Okay, let's go." The two of them flew out the window and into the icy, morning sky. "Ugh," Spike groaned once they were gone. "All this merging stuff is really making me lose beauty sleep."

After an hour flight, they arrived above Canterlot. Not wanting to show Flygon in the streets, the two of them flew high up above the clouds and dove down to the castle gates. The gates were opened, and they stepped inside. Flygon felt that she was starting to feel a bit...weird. Kind of groggy.

In the throne room, Princess Celestia and Princess Luna were waiting. "Glad to see you two made it," Celestia said. "I understand you might be agitated at us."

Flygon stepped forward. "With all due respect, Your Highnesses," she seethed, trying to stay calm. "You can't accept the humans' deal. It threatens me and other Pokémon."

"I feel the same way," Twilight spoke up. "Flygon told me that Pokeballs only hypnotize Pokémon to think they like their masters. It puts them in some sort of trance."

"Does it, really?" Luna, a dark blue alicorn with a starry mane said, narrowing her eyes. "From what I saw, the Pokémon did not seem to be in any sort of trance."

"And just imagine what possibilities this deal could bring to us," Celestia nodded. "With humans and Pokémon at our side, we could do anything. Protecting against dark forces? Constructing cities? Sending mail? All tasks, big and small could be benefited!"

"But...but...Twilight, you can't let this happen!" Flygon cried to the lavender princess.

"Flygon, I know how bad it seems, but they have a point," Twilight said hopelessly.

"Perhaps you need proof on whether the Pokémon are hypnotized," Luna huffed. "Do you wish to see the humans and their captured Pokemon?"

"No way!" Flygon protested. "They'll just capture me!"

"We will guarantee your safety," Celestia promised. "I will tell the humans that they are not allowed to capture you."

"Fine," Flygon gave in. Maybe...the Pokemon weren't hypnotized? But how could that be possible? She would have to see to find out.

The three princesses and the Dragon-Ground Pokemon walked to one of the castle suites up in one of the gleaming white towers. Celestia and Luna went inside the suite, and their voices could be heard telling the humans not to capture Flygon. Three "Yes" voices responded, one female, two male.

"You may come in now," Celestia announced to Flygon. The Pokemon gulped. She couldn't shake this groggy, sluggish state off of her. As Flygon flew into the humongous suite, she studied the three humans who were there warily.

The first looked to be an adult. He was tall, tan skinned, with spiky, dark brown hair and squinty eyes.

The second was a young girl. She had long black hair and pale skin, and held a Piplup in her hands.

And the third...the third...it turned around from where it was talking to a Pikachu. It had fair skin and messy black hair. Suddenly, Flygon realized with a jolt why she was feeling so weird. But it was too late.

"Flygon?" Ash Ketchum gasped. And she felt her eyes glaze over, her brain stop working, and her free will dissipate.

* * *

_**Well, let's see how you guys react to that one! And yes, I chose Brock and Dawn, because they were always my favorite partners.**_


	8. Announcement

_**Sparkers16 here. This announcement is being put up on most of my MLP stories. I've decided to abandon MLP stories on FanFiction.**_

_**Hey, hey, stop right there! I know you were about to make complaining comments on this, but let me explain myself first, mmkay? **_

_**This does NOT mean that I'm stopping my MLP stories. I'm moving them to FimFiction. My reason behind this is that I believe my stories will be more appreciated on Fimfiction than here. I'm not an attention hoarder, but I just feel like this is the right thing to do. My Fimfiction account is also Sparkers16. **_

_**Here is a list of the stories that this announcement affects:**_

_**The Rift**_

_**The Merging**_

_**Six She-Cats**_

_**Nightwing**_

_**Thanks for reading this, and thanks for supporting me, faithful readers.**_


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